相关论文
2023 - International journal of molecular sciences
Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

2021
Wear resistance of HVOF sprayed NiSiCrFeB, WC-Co/NiSiCrFeB, WC-Co, and WC-Cr3C2-Ni rice harvesting blades

Abstract In this work, NiSiCrFeB, WC-Co/NiSiCrFeB, WC-Co, and WC-Cr3C2-Ni coatings were sprayed on rice harvesting blade surfaces using a high velocity oxygen fuel (HVOF) process. Each of the rice harvesting blades was sprayed with one of four coating materials using different spraying durations. The effects of coating materials and spraying durations on the average values of coated blade volume loss, hardness and surface roughness (Ra) were studied through real rice-harvesting field tests. Analysis of variance (ANOVA) and a multiple comparison approach with Tukey’s test were used in order to conduct a comparative performance analysis of the coating materials of rice harvesting blades. The experimental results indicated that the NiSiCrFeB coating exhibited the highest volume loss compared with all others. In addition, the WC-Co-coated blade had significantly greater hardness than those coated with NiSiCrFeB, WC-Co/NiSiCrFeB, or WC-Cr3C2-Ni. The rice harvesting blade coated with either WC-Co/NiSiCrFeB, WC-Co, or WC-Cr3C2-Ni using the shortest spraying duration was recommended for installation in rice harvesting machines.

2014 - Tissue Engineering. Part A
Poly(Epsilon-lysine) dendrons tethered with phosphoserine increase mesenchymal stem cell differentiation potential of calcium phosphate gels.

Calcium phosphates (CaP) are considered as biomaterials of choice for the treatment of critical-sized bone defects. Novel injectable CaP materials integrating poly(epsilon-lysine) generation 3 dendrons tethered with phosphoserine were obtained by sol-gel synthesis. This type of dendron was integrated to mimic the biochemical structure of noncollagenous proteins present in the forming osteoids during bone repair. Sol-gel synthesis was coupled with a dialysis process able to equilibrate the materials at a physiological pH value. Fourier transform infrared spectroscopy (FTIR) showed the successful retention of the dendrons after gel dialysis, whereas X-ray diffraction analysis demonstrated both the pH-tuned formation of a hydroxyapatite crystalline phase within the gel and the complete removal of ammonium nitrate deriving from the sol-gel reaction solvent. Scanning electron microscopy images confirmed the presence of crystalline domains in gels synthesized at pH 9.0. Injectability tests showed that the optimized formulations fulfilled the rheological properties required to minimally invasive surgical procedures. Cytotoxicity tests on osteoblast-like MG-63 cells as well as morphology and viability studies showed that the dendrons induced a significantly higher level of cell proliferation at early incubation time. Differentiation of the cell was also clearly enhanced at longer incubation time as demonstrated by both alkaline phosphatase activity and expression of typical markers. Altogether, the data from this work indicate the clinical potential of the osteoid-mimicking CaP cements in minimally invasive bone surgery.

2015
GROW OUT TEST AND DETERMINATION OF PHYSICAL CHARACTERISTICS OF SEED OF RICE LANDRACES

The study was attempted with an objective to check the purity of commonly used farmer’s rice seed stock. Assessment of varietal purity of collected 76 rice genotypes showed that there was a variation among the genotypes for varietal purity. Thirty-two genotypes showed 100% varietal purity and forty-four genotypes were contaminated with different types of offtypes. The lowest varietal purity was observed in Lal gotal (74.67%). Grain dimension and 1000 seed weight were measured as important physical characteristics of seed to identify varietal purity.

2015 - Journal of Biomolecular Structure and Dynamics
A method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis

Lysine acetylation and ubiquitination are two primary post-translational modifications (PTMs) in most eukaryotic proteins. Lysine residues are targets for both types of PTMs, resulting in different cellular roles. With the increasing availability of protein sequences and PTM data, it is challenging to distinguish the two types of PTMs on lysine residues. Experimental approaches are often laborious and time consuming. There is an urgent need for computational tools to distinguish between lysine acetylation and ubiquitination. In this study, we developed a novel method, called DAUFSA (distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis), to discriminate ubiquitinated and acetylated lysine residues. The method incorporated several types of features: PSSM (position-specific scoring matrix) conservation scores, amino acid factors, secondary structures, solvent accessibilities, and disorder scores. By using the mRMR (maximum relevance minimum redundancy) method and the IFS (incremental feature selection) method, an optimal feature set containing 290 features was selected from all incorporated features. A dagging-based classifier constructed by the optimal features achieved a classification accuracy of 69.53%, with an MCC of .3853. An optimal feature set analysis showed that the PSSM conservation score features and the amino acid factor features were the most important attributes, suggesting differences between acetylation and ubiquitination. Our study results also supported previous findings that different motifs were employed by acetylation and ubiquitination. The feature differences between the two modifications revealed in this study are worthy of experimental validation and further investigation.

1984 - European journal of biochemistry
A novel form of gastric inhibitory polypeptide (GIP) isolated from bovine intestine using a radioreceptor assay. Fragmentation with staphylococcal protease results in GIP1-3 and GIP4-42, fragmentation with enterokinase in GIP1-16 and GIP17-42.

A novel form of gastric inhibitory polypeptide (GIP), later also referred to as glucose-dependent insulinotropic polypeptide, has been isolated from bovine upper intestine. The purification was monitored by a recently developed radioreceptor assay, specific for GIP, using membrane preparations from hamster beta-cell tumors. A combination of ion-exchange and reverse-phase high-performance liquid chromatography was used in the isolation which resulted in homogeneous bovine GIP. Bovine GIP is, like porcine GIP, composed of 42 amino acid residues. The sequence is: Tyr-Ala-Glu-Gly-Thr-Phe-Ile-Ser-Asp-Tyr-Ser-Ile-Ala-Met-Asp-Lys-Ile-Arg- Gln-Gln - Asp-Phe-Val-Asn-Trp-Leu-Leu-Ala-Gln-Lys-Gly-Lys-Lys-Ser-Asp-Trp-Ile-His- Asn-Ile - Thr-Gln, which differs from that of the previously characterized porcine GIP by having isoleucine instead of lysine at position 37. Upon proteolytic digestion of GIP with the staphylococcal V8 protease and with enterokinase, two fragments are formed in each case, corresponding to GIP1-3, GIP4-42, and GIP1-16, GIP17-42, respectively.

2019 - Journal of Cognitive Neuroscience
Intracranial Recordings and Computational Modeling of Music Reveal the Time Course of Prediction Error Signaling in Frontal and Temporal Cortices

Prediction is held to be a fundamental process underpinning perception, action, and cognition. To examine the time course of prediction error signaling, we recorded intracranial EEG activity from nine presurgical epileptic patients while they listened to melodies whose information theoretical predictability had been characterized using a computational model. We examined oscillatory activity in the superior temporal gyrus (STG), the middle temporal gyrus (MTG), and the pars orbitalis of the inferior frontal gyrus, lateral cortical areas previously implicated in auditory predictive processing. We also examined activity in anterior cingulate gyrus (ACG), insula, and amygdala to determine whether signatures of prediction error signaling may also be observable in these subcortical areas. Our results demonstrate that the information content (a measure of unexpectedness) of musical notes modulates the amplitude of low-frequency oscillatory activity (theta to beta power) in bilateral STG and right MTG from within 100 and 200 msec of note onset, respectively. Our results also show this cortical activity to be accompanied by low-frequency oscillatory modulation in ACG and insula—areas previously associated with mediating physiological arousal. Finally, we showed that modulation of low-frequency activity is followed by that of high-frequency (gamma) power from approximately 200 msec in the STG, between 300 and 400 msec in the left insula, and between 400 and 500 msec in the ACG. We discuss these results with respect to models of neural processing that emphasize gamma activity as an index of prediction error signaling and highlight the usefulness of musical stimuli in revealing the wide-reaching neural consequences of predictive processing.

2007 - PLoS ONE
Global Profiling of DNA Replication Timing and Efficiency Reveals that Efficient Replication/Firing Occurs Late during S-Phase in S. pombe

Background During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins) that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. Methodology/Principal Findings Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Δ cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Δ cells after HU removal, owing to the firing at the remaining unused (inefficient) origins during HU treatment. Conclusions/Significance Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

1996 - The Biochemical journal
Characterization of structural determinants and molecular mechanisms involved in pro-stromelysin-3 activation by 4-aminophenylmercuric acetate and furin-type convertases.

Stromelysin-3 (ST3) is a matrix metalloproteinase (MMP) which has been implicated in cancer progression and in a number of conditions involving tissue remodelling. In contrast to other MMPs which are secreted as zymogens requiring extracellular activation, ST3 is found in the extracellular space as a potentially active mature form, suggesting that the activation of the ST3 proform differs from that of other MMPs. We show in the present study that the ST3 proform is not autocatalytically processed in the presence of 4-aminophenylmercuric acetate (APMA). By using ST3/ST2 chimeras, we demonstrate that resistance to APMA is due to properties associated with both the ST3 pro- and catalytic domains. In agreement with the observation made by Pei and Weiss [Pei and Weiss (1995) Nature (London) 375, 244-247], we find that the requirement for activation of the ST3 proform by the furin convertase is entirely contained within a stretch of 10 amino acids located at the junction between the ST3 pro- and catalytic domains. Furin cleaves human and mouse ST3 equally well. However, PACE-4, a furin-like convertase, is much more efficient on the mouse enzyme, suggesting that ST3 protein determinants other than the conserved Ala-Arg-Asn-Arg-Gln-Lys-Arg sequence preceding the furin cleavage site are implicated in PACE-4 action. Finally, we show that processing of the ST3 proform is inhibited by a furin inhibitor in human MCF7 breast cancer cells stably transfected to constitutively express a full-length human ST3 cDNA. Using brefeldin A, we demonstrate that, in these MCF7 cells, the 56 kDa precursor form of ST3 is post-translationally modified in the cis- or media-Golgi into a 62 kDa proform. Thereafter, its processing into the 47 kDa mature form occurs in the trans-Golgi network and is followed by secretion into the extracellular space.

2004
Machine vision inspection of rice seed based on Hough transform

A machine vision system was developed to inspect the quality of rice seeds. Five varieties of Jinyou402,Shanyou 10, Zhongyou207, Jiayou and Ilyou were evaluated. The images of both sides of rice seed with black background and white background were acquired with the image processing system for identifying external features of rice seeds. Five image sets consisting of 600 original images each were obtained. Then a digital image processing algorithm based on Hough transform was developed to inspect the rice seeds with incompletely closed glumes. The algorithm was implemented with all image sets using a Matlab 6.5 procedure. The results showed that the algorithm achieved an average accuracy of 96% for normal seeds, 92% for seeds with fine fissure and 87% for seeds with incompletely closed glumes. The algorithm was proved to be applicable to different seed varieties and insensitive to the color of the background.

1967
STUDIES ON THE ENVIRONMENTAL FLUCTUATION OF GERMINATION HABITS OF RICE SEEDS AND THE TEST AND SELECTION METHODS FOR THEM : I. On the effect of temperature during maturation on germination of rice seeds

Considerable dormancy or delayed germination was found to be induced, when the rice seeds matured at relatively low temperature in the early stage of maturation and at high temperature (about 30°C. or more) in the latter half of that period. In contrast to this fact, the germination speed was accelerated by the high temperature 5 or 10 days after ear emergence. These facts were observed equally in three varieties differentiating each other in germination habit.

2006
Evaluation of Transgenic Rice Expressing Cry1Ac and CpTI Against Chilo suppressalis and Intrapopulation Variation in Susceptibility to Cry1Ac

Abstract The field efficacy of two transgenic rice lines, containing the Cry1Ac gene from Bacillus thuringiensis (Bt) and the CpTI (cowpea trypsin inhibitor) gene, on the striped stem borer, Chilo suppressalis (Walker), and population variation in susceptibility of C. suppressalis to the Bt insecticidal protein Cry1Ac were evaluated in Fuzhou, Fujian Province of China. The results of an open field test showed that the two transgenic lines exhibited high efficacy against natural infestations of C. suppressalis. In contrast, the untransformed parental control line showed serious damage symptoms not only in untreated plots, but also in plots treated with insecticides. The cumulative number of C. suppressalis adults derived from transgenic rice lines was significantly lower than that from control lines with and without chemical control treatments. Our results show that transgenic rice lines expressing Cry1Ac and CpTI have great potential for protecting rice from C. suppressalis damage with reduced use of insecticides. Comparison of pupal weight and fecundity of C. suppressalis between transgenic and control treatments indicated that pupal weight significantly decreased after continuously feeding on transgenic rice lines, but there was no significant effect on fecundity. Adult females of C. suppressalis were collected from light traps to ascertain population variation in susceptibility to Bt toxins. Each female producing enough fertile eggs for bioassays was used as the parent of an isofemale line. Of 1,100 females collected, 395 isofemale lines produced enough offspring to be screened on a diet assay treated with Cry1Ac. The results showed that 51.7% of isofemale lines were differentiated as highly susceptible, 23.0% as moderately susceptible, and 23.8% with low susceptibility; 1.5% were nonsusceptible, with a survival rate >70% and similar development as on the non-Bt control diet. The results indicated significant variation in susceptibility to Cry1Ac in the C. suppressalis population, which should be considered for insect resistance management of Bt rice in the future.

1992 - British Journal of Nutrition
Evaluation of the nutritive value of yellow rice in rats and broiler chicks

Yellow discoloration often develops in rice kernels during post-harvest storage, due possibly to fungal activity. The present study examined the changes in nutrient composition taking place during yellowing of rice, and the effects of feeding rats and broiler chicks on a moderately yellow rice at 600 g/kg diet. Nitrogen content was found to be higher in rice grains that had become more yellow, only part of the increase being in non-protein-N; however, relative to crude protein (N x 6.25) the concentrations of lysine, methionine, cystine and arginine were lower. There were no significant differences between white and yellow rice in the food intake, weight gain and efficiency of food utilization (EFU) of rats and chicks when diets were formulated to contain similar nutrient concentrations, or the same basal ingredient composition. Diet pelleting increased food intake and weight gain in both animal species, but reduced dry matter and energy digestibility in rats; effects on nutrient retention in chicks were largely non-significant. Liver weights of rats and chicks and pancreas weights of chicks were unaffected by yellow rice; however, chicks fed on mash had a larger pancreas on average than those fed on pellets. Thus, whilst the nutrient composition of rice is altered during yellowing, a moderately yellow rice is unlikely to produce major adverse effects when fed to rats and broiler chicks.

1999 - Plant disease
The Genetic Basis of High Resistance to Rice Yellow Mottle Virus (RYMV) in Cultivars of Two Cultivated Rice Species.

Three cultivars of Oryza sativa (IR64, Azucena, and Gigante) and four cultivars of O. glaberrima (Tog5681, Tog5673, CG14, and SG329) were evaluated for their resistance to two isolates of rice yellow mottle virus (RYMV) by enzyme-linked immunosorbent assay (ELISA) and symptomatology. Cultivars Tog5681 and Gigante were highly resistant, and no symptoms were observed when either virus isolate was inoculated at 10 or 20 days postgermination and assayed by ELISA at 7, 14, 22, 35, 50, or 64 days postinoculation. Azucena showed a partial resistance, whereas the other cultivars were susceptible. Symptom appearance was associated with increase in ELISA absorbance in the systemically infected leaves. The best discrimination among the cultivars occurred when the plants were inoculated at 10 days postgermination. Crosses were made between the highly resistant (Gigante and Tog5681) and the susceptible (IR64) cultivars to determine the genetic basis of resistance to RYMV. Evaluation of F1 hybrids and interspecific progenies, as well as the segregation of resistance in F2 and F3 lines of the IR64 × Gigante cross, provided results consistent with the presence of a single recessive resistance gene common to Tog5681 and Gigante.

2016 - 2016 IEEE RIVF International Conference on Computing & Communication Technologies, Research, Innovation, and Vision for the Future (RIVF)
Spatial and spectral features utilization on a Hyperspectral imaging system for rice seed varietal purity inspection

A conventional method to inspect the varietal purity of rice seeds is based on human visual inspection where a random sample is drawn from a batch. This is a tedious, laborious, time consuming and extremely inefficient task. This paper presents an automatic rice seed inspection method using Hyperspectral imaging and machine learning, to automatically detect unwanted seeds from other varieties which may be contained in a batch. Hyperspectral image data from Near-infrared (NER) camera are acquired for six common rice seed varieties. The results of applying two classifiers are presented, a Support Vector Machine (SVM) and a Random Forest (RF), where each consists of six one-versus-rest binary classifiers. The results show that combining spectral and shape-based features derived from the rice seeds, increase precision of the multi-label classification to 84% compared 74% when only visual features are used.

2016
Investigation of Hg uptake and transport between paddy soil and rice seeds combining Hg isotopic composition and speciation

Human consumption of rice constitutes a potential toxicological risk in mercury (Hg) polluted areas such as Hg mining regions in China. It is recognized to be an important source of Hg for the local human diet considering the efficient bioaccumulation of methylmercury (MeHg) in rice seed. To assess Hg sources and uptake pathways to the rice plants, Hg speciation and isotopic composition were investigated in rice seeds and their corresponding paddy soils from different locations within the Wanshan Hg mining area (Guizhou Province, China). A large variation of Hg speciation is observed in rice seeds and paddy soils irrespective of the sampling location. Mass dependent fractionation (MDF) of Hg in rice seeds differs by up to ∼4.0 ‰ in δ202Hg values, while mass independent fractionation (MIF) of Hg isotopes remains constant (Δ199Hg ∼ 0‰). Hg isotopic composition in rice seeds covaries with that of paddy soils but exhibits lighter isotopic signature (δ202Hg). Such isotopic offset is mainly attributed to plant uptake and translocation processes. Also, seeds containing higher MeHg (MeHg/total Hg > 50%) have significantly heavier Hg isotopes suggesting that MeHg uptake and transport to the seed in such rice plants is facilitated compared to inorganic Hg.

2008 - Nucleic Acids Research
Characterization and expression profiles of miRNAs in rice seeds

Small RNAs (sRNAs) are common and effective modulators of gene expression in eukaryotic organisms. To characterize the sRNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 797 399 22-nt sequence signatures, of which 111 161 are distinct ones. Analysis on the distributions of sRNAs on chromosomes showed that most sRNAs originate from interspersed repeats that mainly consist of transposable elements, suggesting the major function of sRNAs in rice seeds is transposon silencing. Through integrative analysis, 26 novel miRNAs and 12 miRNA candidates were identified. Further analysis on the expression profiles of the known and novel miRNAs through hybridizing the generated chips revealed that most miRNAs were expressed preferentially in one or two rice tissues. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated. In addition, differential accumulations of miRNAs and corresponding miRNA*s suggest the functions of miRNA*s other than being passenger strands of mature miRNAs, and in regulating the miRNA functions.

2010 - Plant Physiology
Characterization of the Rice PHO1 Gene Family Reveals a Key Role for OsPHO1;2 in Phosphate Homeostasis and the Evolution of a Distinct Clade in Dicotyledons1[C][W][OA]

Phosphate homeostasis was studied in a monocotyledonous model plant through the characterization of the PHO1 gene family in rice (Oryza sativa). Bioinformatics and phylogenetic analysis showed that the rice genome has three PHO1 homologs, which cluster with the Arabidopsis (Arabidopsis thaliana) AtPHO1 and AtPHO1;H1, the only two genes known to be involved in root-to-shoot transfer of phosphate. In contrast to the Arabidopsis PHO1 gene family, all three rice PHO1 genes have a cis-natural antisense transcript located at the 5 ′ end of the genes. Strand-specific quantitative reverse transcription-PCR analyses revealed distinct patterns of expression for sense and antisense transcripts for all three genes, both at the level of tissue expression and in response to nutrient stress. The most abundantly expressed gene was OsPHO1;2 in the roots, for both sense and antisense transcripts. However, while the OsPHO1;2 sense transcript was relatively stable under various nutrient deficiencies, the antisense transcript was highly induced by inorganic phosphate (Pi) deficiency. Characterization of Ospho1;1 and Ospho1;2 insertion mutants revealed that only Ospho1;2 mutants had defects in Pi homeostasis, namely strong reduction in Pi transfer from root to shoot, which was accompanied by low-shoot and high-root Pi. Our data identify OsPHO1;2 as playing a key role in the transfer of Pi from roots to shoots in rice, and indicate that this gene could be regulated by its cis-natural antisense transcripts. Furthermore, phylogenetic analysis of PHO1 homologs in monocotyledons and dicotyledons revealed the emergence of a distinct clade of PHO1 genes in dicotyledons, which include members having roles other than long-distance Pi transport.

2013 - Cell
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

N(6)-methyladenosine (m(6)A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m(6)A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of eight methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time course and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminate a conserved, dynamically regulated methylation program in yeast meiosis and provide an important resource for studying the function of this epitranscriptomic modification.

2008 - Science
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.

Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed.

Zhongyi Cheng
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Dongli He
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Rebecca Njeri Damaris
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Pingfang Yang
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Ming Li
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Pingfang Yang
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Zhongyi Cheng
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Dongli He
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Xingling Yi
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Qiong Wang
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R. N. Damaris
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Qiong Wang
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Ming Li
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Xingling Yi

Abstract:Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.

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引用
First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence
Frontiers in Cellular and Infection Microbiology
2021
Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation.
Biochimica et biophysica acta. Proteins and proteomics
2018
First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L.
Scientific Reports
2016
Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)
Molecules
2018
Effects of PSII Manganese-Stabilizing Protein Succinylation on Photosynthesis in the Model Cyanobacterium Synechococcus sp. PCC 7002
Plant & cell physiology
2018
Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites
Cells
2019
Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds
Scientific Reports
2017
Malonylome analysis in developing rice (Oryza sativa) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially.
Journal of proteomics
2018
Proteomic analysis of lysine succinylation of the human pathogen Histoplasma capsulatum.
Journal of proteomics
2017
Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis
Molecular systems biology
2017
Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos
PloS one
2017
Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives
International journal of molecular sciences
2020
Lysine acetylation in mitochondria: From inventory to function.
Mitochondrion
2017
Global analysis of protein lysine succinylation profiles in common wheat
BMC Genomics
2017
Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway
BMC Genomics
2017
The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes
BMC Genomics
2017
Global Phosphoproteomic Analysis Reveals the Involvement of Phosphorylation in Aflatoxins Biosynthesis in the Pathogenic Fungus Aspergillus flavus
Scientific Reports
2016
Lysine Succinylation Contributes to Aflatoxin Production and Pathogenicity in Aspergillus flavus*
Molecular & Cellular Proteomics
2018
Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria.
Journal of proteome research
2017
Peroxiredoxins and Redox Signaling in Plants
Antioxidants & redox signaling
2017